Over at WMW, Googleguy discusses one aspect of the problems people are seeing regarding crawling, indexing, and supplementals. Unfortunately, he only focused in on one small part of the whole thing, so there are still tons of questions to be answered. Nevertheless, those of you who are seeing strange things should head over there and read up about it. One of the things he mentioned:
We've been refreshing some (but not all) of the supplemental results. One part of the supplemental indexing system didn't return any results for [site:domain.com] (that is, a site: search with no additional terms). So that would match with fewer results being reported for site: queries but traffic not changing much. The pages are available for queries matching the supplemental results, but just adding a term or stopword to site: wouldn't automatically access those supplemental results.
He also gives the email address to write to if your situation fits with what he is discussing. You can see all of his comments here.